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We present an efficient point-particle approach to simulate reaction-diffusion processes of spherical absorbing particles in the diffusion-limited regime, as simple models of cellular uptake. The exact solution for a single absorber is used to calibrate the method, linking the numerical parameters to the physical particle radius and uptake rate. We study configurations of multiple absorbers of increasing complexity to examine the performance of the method, by comparing our simulations with available exact analytical or numerical results. We demonstrate the potentiality of the method in resolving the complex diffusive interactions, here quantified by the Sherwood number, measuring the uptake rate in terms of that of isolated absorbers. We implement the method in a pseudo-spectral solver that can be generalized to include fluid motion and fluid-particle interactions. As a test case of the presence of a flow, we consider the uptake rate by a particle in a linear shear flow. Overall, our method represents a powerful and flexible computational tool that can be employed to investigate many complex situations in biology, chemistry and related sciences.
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The biotransport of the intravascular nanoparticle (NP) is influenced by both the complex cellular flow environment and the NP characteristics. Being able to computationally simulate such intricate transport phenomenon with high efficiency is of far-reaching significance to the development of nanotherapeutics, yet challenging due to large length-scale discrepancies between NP and red blood cell (RBC) as well as the complexity of NP dynamics. Recently, a lattice-Boltzmann (LB) based multiscale simulation method has been developed to capture both NP scale and cellular level transport phenomenon at high computational efficiency. The basic components of this method include the LB treatment for the fluid phase, a spectrin-link method for RBCs, and a Langevin dynamics (LD) approach to capturing the motion of the suspended NPs. Comprehensive two-way coupling schemes are established to capture accurate interactions between each component. The accuracy and robustness of the LB-LD coupling method are demonstrated through the relaxation of a single NP with initial momentum and self-diffusion of NPs. This approach is then applied to study the migration of NPs in a capillary vessel under physiological conditions. It is shown that Brownian motion is most significant for the NP distribution in capillary vessels. For 1~100 nm particles, the Brownian diffusion is the dominant radial diffusive mechanism compared to the RBC-enhanced diffusion. For ~500 nm particles, the Brownian diffusion and RBC-enhanced diffusion are comparable drivers for the particle radial diffusion process.
We propose a one-way coupled model that tracks individual primary particles in a conceptually simple cellular flow setup to predict flocculation in turbulence. This computationally efficient model accounts for Stokes drag, lubrication, cohesive and direct contact forces on the primary spherical particles and allows for a systematic simulation campaign that yields the transient mean floc size as a function of the governing dimensionless parameters. The simulations reproduce the growth of the cohesive flocs with time, and the emergence of a log-normal equilibrium distribution governed by the balance of aggregation and breakage. Flocculation proceeds most rapidly when the Stokes number of the primary particles is textit{O}(1). Results from this simple computational model are consistent with experimental observations, thus allowing us to propose a new analytical flocculation model that yields improved agreement with experimental data, especially during the transient stages.
This work presents a new multiphase SPH model that includes the shifting algorithm and a variable smoothing length formalism to simulate multi-phase flows with accuracy and proper interphase management. The implementation was performed in the DualSPHysics code and validated for different canonical experiments, such as the single-phase and multiphase Poiseuille and Couette test cases. The method is accurate even for the multiphase case for which two phases are simulated. The shifting algorithm and the variable smoothing length formalism has been applied in the multiphase SPH model to improve the numerical results at the interphase even when it is highly deformed and non-linear effects become important. The obtained accuracy in the validation tests and the good interphase definition in the instability cases indicate an important improvement in the numerical results compared with single-phase and multiphase models where the shifting algorithm and the variable smoothing length formalism are not applied.
In this study we investigated the capabilities of the mesh-free, Lagrangian particle method (Smoothed Particle Hydrodynamics, SPH) to simulate the detailed hydrodynamic processes generated by both spilling and plunging breaking waves within the surf zone. The weakly-compressible SPH code DualSPHysics was applied to simulate wave breaking over two distinct bathymetric profiles (a plane beach and fringing reef) and compared to experimental flume measurements of waves, flows, and mean water levels. Despite the simulations spanning very different wave breaking conditions (including an extreme case with violently plunging waves on an effectively dry reef slope), the model was able to reproduce a wide range of relevant surf zone hydrodynamic processes using a fixed set of numerical parameters. This included accurate predictions of the nonlinear evolution of wave shapes (e.g., asymmetry and skewness properties), rates of wave dissipation within the surf zone, and wave setup distributions. By using this mesh-free approach, the model was able to resolve the critical crest region within the breaking waves, which provided robust predictions of the wave-induced mass fluxes within the surf zone responsible for the undertow. Within this breaking crest region, the model results capture how the potential energy of the organized wave motion is initially converted to kinetic energy and then dissipated, which reproduces the distribution of wave forces responsible for wave setup generation across the surf zone. Overall, the results reveal how the mesh-free SPH approach can accurately reproduce the detailed wave breaking processes with comparable skill to state-of-the-art mesh-based Computational Fluid Dynamics (CFD) models, and thus can be applied to provide valuable new physical insight into surf zone dynamics.
Smoldering combustion plays an important role in forest and wildland fires. Fires from smoldering combustion can last for long periods of time, emit more pollutants, and be difficult to extinguish. This makes the study of smoldering in woody fuels and forest duff important. Cellulose, hemicellulose, and lignin are the major constituents in these type of fuels, in different proportions for different fuels. In this paper, we developed a 1-D model using the open-source software Gpyro to study the smoldering combustion of cellulose and hemicellulose mixtures. We first validated our simulations against experimentally obtained values of propagation speed for mixtures with fuel compositions including 100%, 75%, 50%, and 25% cellulose, with the remaining proportion of hemicellulose. Then, we studied the effects of varying fuel composition, density, and moisture content on smoldering combustion. We find that propagation speed of smoldering increased with decreases in density and increases in hemicellulose content, which we attribute to the role of oxygen diffusion. Propagation speed increased with moisture content for pure cellulose up to a certain limiting value, after which the propagation speed dropped by up to 70%. The mean peak temperature of smoldering increased with increases in hemicellulose content and density, and decreased with increasing moisture content.
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